Comments (3)
idxdepth and "sd depth" are not the same thing.
"idxdepth" is the path to the output from running idxdepth, the depth estimation tool.
"depth sd" is the square root of "depth variance", used as a parameter in genotyping. If neither "depth variance" nor "depth sd" is specified, Paragraph will estimate that from your "depth" input.
I need to fix the error message and README.
from paragraph.
That's what I thought, and just to clarify I added those extra columns since I wanted Paragraph to know the sex of my samples since I am also using the X chromosome in genotyping. Therefore, I needed to put in those "depth sd" and "depth variance"
from paragraph.
Fix included in v2.4. now "depth sd" can be correctly recognized in manifest.
If you have "sex" column in the manifest, Paragraph will automatically adjust depth in chrX and chrY.
from paragraph.
Related Issues (20)
- Missing key SEQ for <INS> HOT 6
- --vcf-split option with no description
- subprocess.CalledProcessError HOT 2
- grmpy error: [E::cram_itr_query]
- index file
- How to merge multi-samples SVs and obtain breakpoints for genotyping a population
- no BGZF EOF marker
- Install paragraph
- Stop using Werror and Wall
- Genotyping for SNP
- idxdepth regex option not working
- Problem starting the script multigrmpy.py HOT 2
- Error when working with `--ins-info-key` HOT 1
- Add support for VCFv4.2 breakend notation
- Issue's with Native Build and Boost
- Format error in vcf line: HOT 3
- [BUG] Error adding alt from insertion sequence representing a duplication
- Distance between vcf position and chrom start is smaller than read length.
- BAM header only has a subset of the reference chromosomes -- please make sure they match!
- Whole Exome Data?
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from paragraph.